{"entity":{"id":"gsea","kind":"term","name":"Gene set enrichment analysis (GSEA and ssGSEA)","aka":["gene set enrichment analysis","gene set enrichment","GSEA","ssGSEA","single-sample GSEA","pathway enrichment","enrichment analysis","enrichment score"],"tldr":"Gene set enrichment analysis asks whether the genes that changed in an experiment cluster in a known pathway or signature, turning a list of genes into a biological story.","summary":"Gene set enrichment analysis identifies classes of genes that are over-represented in a large gene list and may be associated with a phenotype (Wikipedia); Subramanian and colleagues' GSEA ranks all genes by association with a phenotype and tests whether a set concentrates at the top or bottom. Single-sample GSEA, introduced by Barbie and colleagues, scores one sample at a time, producing per-patient pathway activity scores that can be model features. The gene sets come from MSigDB (hallmark, KEGG, Reactome, GO collections). Enrichment describes; it does not prove mechanism.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/Gene_set_enrichment_analysis","links":[{"label":"Subramanian et al., Gene set enrichment analysis (PNAS 2005)","url":"https://doi.org/10.1073/pnas.0506580102"},{"label":"Barbie et al., ssGSEA introduced in Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 (Nature 2009)","url":"https://doi.org/10.1038/nature08460"},{"label":"MSigDB","url":"https://www.gsea-msigdb.org/gsea/msigdb/"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Gene_set_enrichment_analysis"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":[],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["pathway-activation-state","gene-co-expression"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":["Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/gsea-ssgsea."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme"},"category":"Genomics & genetics"},"route":"/terms/gsea/","neighbours":{"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"gene-co-expression","kind":"term","name":"Gene co-expression structure","route":"/terms/gene-co-expression/"},{"id":"pathway-activation-state","kind":"term","name":"Pathway activation state (phosphosignalling)","route":"/terms/pathway-activation-state/"}]}}